The failure of the pilot of the other airplane to correctly set a new transponder code and an anomaly in ATC software that precluded the controller from manually overriding the resulting inhibition of displayed data. Factors in the accident were impaired function of the collision avoidance system in the airplane due to structural masking of the other airplane's transponder antenna, an intermittent failure of the approach controller's communication radio transmitter which interfered with his ability to communicate traffic information to the pilots, the failure of both the approach controller and the tower controller to issue safety alerts when the traffic conflict became apparent, and the failure of the flight crew to maintain an adequate visual lookout to see and avoid the other airplane.